Evaluate gene sets identified by SDAN
Wei Sun
2024-07-12
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 23.00 24.00 25.00 24.55 25.00 26.00## [1] 40## [1] 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 25 25 25 25 25 25 25
## [26] 25 25 25 25 25 25 26 26 26 26 26 26 26 26 26## [1] 982Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"##
## FALSE TRUE
## 1120 139##
## FALSE TRUE <NA>
## 71 1049 139gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7## t1
## 1 2
## 1255 2## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"## reactome go_bp immune
## 1692 7647 5219Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992Conduct enrichment analysis
## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MTIF2" "KHSRP" "MRPS33" "NDUFAF5" "CDK5RAP1" "EARS2"
## [7] "MTFMT" "SARS2" "GTPBP10" "DHX58" "ATPAF1" "NDUFAF4"
## [13] "C6orf203" "MTO1" "MRRF" "MALSU1" "MRPL55" "NDUFS4"
## [19] "PHAX" "MRPL48" "ZNF431" "MRPL23" "CCDC109B"
## [1] 2
## [1] "CENPQ" "CENPO" "ZNF816" "RPS17" "TNF" "APBA2" "RPL34"
## [8] "RPS12" "RASGRF2" "EGR1" "RPL21" "FOSB" "JUND" "SORL1"
## [15] "RPS27A" "RPL9" "RBKS" "JUNB" "RPLP2" "RPS27" "DNHD1"
## [22] "RPS23" "RPS18"
## [1] 3
## [1] "MAD1L1" "SLC25A14" "ERCC2" "IMPDH1" "C17orf75" "GTF2H3"
## [7] "CDC20" "DCAF4" "CKS2" "MCEE" "UROD" "PDZD2"
## [13] "CCNB1" "CDK7" "COPS3" "CCNB2" "MTHFD2L" "POLE"
## [19] "BTLA" "HIST1H4J" "PRIM1" "C1orf85" "STK19" "MUC20"
## [1] 4
## [1] "DERL2" "SMUG1" "GLUL" "TMOD3" "LINS" "PLIN2"
## [7] "MZT2B" "HIST1H2BD" "GLB1" "KBTBD2" "IFRD2" "C17orf89"
## [13] "PPIL3" "IFRD1" "PIK3IP1" "YPEL5" "BTG1" "SLC38A2"
## [19] "SKIL" "PDCD4" "FAM102A" "PFKFB3" "RALGAPA1"
## [1] 5
## [1] "TBPL1" "NT5C2" "WDR13" "IFI6"
## [5] "XAF1" "TMEM241" "APH1B" "WARS"
## [9] "GTF2A2" "TATDN1" "LZTFL1" "TRIM68"
## [13] "GTSF1" "FCRL6" "PSMG1" "UBXN2B"
## [17] "TSTD1" "TRGC2" "PATL2" "TRGV2"
## [21] "AC092580.4" "RP11-552M11.4" "HMGB1P24" "AC139149.1"
## [25] "CTD-3214H19.4"
## [1] 6
## [1] "MFAP3" "FAR2" "CAPN15" "PIEZO1" "POP4" "CD86"
## [7] "CD160" "DHDDS" "NPC2" "IFIT3" "IFIT2" "NME2P1"
## [13] "L3HYPDH" "HRSP12" "PRMT7" "DPH6" "C1orf123" "CTLA4"
## [19] "POP5" "IFIT1" "TMEM120A" "POTEKP" "PVT1"
## [1] 7
## [1] "KHDC1" "ABHD16B" "ZNF93" "NPM1P33"
## [5] "RP11-247I13.3" "RP11-270C12.3" "PGAM4" "PIN4P1"
## [9] "RP11-247I13.6" "SEPT7P7" "PA2G4P4" "RP11-782C8.1"
## [13] "BTF3P10" "RPS27AP2" "AC007041.2" "RPS19P3"
## [17] "RN7SL56P" "GAPDHP60" "RNF138P1" "KB-1507C5.2"
## [21] "SLC2A3P4" "HSPA8P5" "ANP32AP1" "CTB-52I2.4"
## [25] "CTD-2545M3.2" "RP4-739H11.4"
## [1] 8
## [1] "MAP4K5" "KIF4A" "SPTLC2" "RAD51C"
## [5] "MCM9" "SMC4" "CACYBP" "AKR1A1"
## [9] "CCR2" "TEP1" "NPHP4" "SLC2A8"
## [13] "HIRIP3" "RNF207" "LRRC28" "PLA2G6"
## [17] "EFCAB7" "HSPA1B" "TRAV21" "NAP1L1P3"
## [21] "RP11-773D16.1" "RP11-307P22.1" "CTD-2521M24.9" "C1orf63"
## [25] "RP11-727F15.9"
## [1] 9
## [1] "VPS41" "SH3BP2" "DEPDC5" "ARHGEF18" "LIG1" "DDX49"
## [7] "BRD8" "NPRL2" "CHTF18" "TPGS2" "ACTL6A" "MTF2"
## [13] "SUV39H2" "FARP1" "CXXC1" "TAF10" "TRAPPC11" "RMDN1"
## [19] "TECPR1" "SSH2" "PIP4K2A" "BRD2" "PPP1R10"
## [1] 10
## [1] "PTPN18" "MAP3K13" "ZNF684" "TXNDC17"
## [5] "PUS7L" "TROAP" "GEMIN6" "MPPE1"
## [9] "KIAA1841" "CTSB" "C11orf82" "TBCA"
## [13] "ZBED2" "GEN1" "TMEM194B" "RP11-64B16.2"
## [17] "NCKIPSD" "AC098614.2" "RPF2P1" "CCT8P1"
## [21] "BDH2P1" "GAPDHP2" "RP11-844P9.3" "PAICSP4"
## [25] "RP11-473N11.2"
## [1] 11
## [1] "CD84" "ZNF85" "GALK1" "MS4A6A"
## [5] "STK25" "CCRL2" "STYXL1" "NARG2"
## [9] "TMEM138" "ZBTB39" "ZNF613" "SPATA13"
## [13] "CCDC30" "RP11-12M9.4" "HNRNPKP2" "RP3-342P20.2"
## [17] "PA2G4P2" "AC002331.1" "HNRNPA1P55" "CCL3L3"
## [21] "RBBP4P5" "HMGB1P8" "HNRNPA1P16" "CTB-31O20.3"
## [25] "RP11-686D22.10"
## [1] 12
## [1] "TM7SF3" "TIPIN" "TIMM9" "PLA2G15" "GABPB1"
## [6] "DOT1L" "ZNF419" "DUS4L" "LOXL3" "FANCL"
## [11] "TIMM10" "RNF121" "CCDC28B" "RNF25" "PRIMPOL"
## [16] "CDCA7L" "SESTD1" "TDRD7" "GM2A" "CHAMP1"
## [21] "FANCG" "GK3P" "RP11-402J6.3" "ATP5A1P3"
## [1] 13
## [1] "PIM2" "HAVCR1" "PECR" "USF1" "FCRL3"
## [6] "WDR41" "NAALADL1" "AC004840.9" "COA3" "CMC1"
## [11] "CCL3L1" "RAB12" "TRAV24" "RP11-2F9.3" "MIR29B1"
## [16] "PET100" "RP11-693N9.2" "LINC00426" "RN7SL749P" "AC005329.7"
## [21] "AP000462.1" "SNORD3A" "C9orf72" "MS4A1"
## [1] 14
## [1] "DYRK4" "GLT8D1" "ID3" "MFSD9"
## [5] "TMEM19" "NTAN1" "TMSB15B" "ZNF511"
## [9] "RP13-383K5.4" "CD27-AS1" "UBA52P6" "ACTBP8"
## [13] "RPL19P12" "ARPC3P1" "PHBP3" "ATF4P3"
## [17] "TCP1P1" "TPI1P2" "ETF1P2" "RPL13P5"
## [21] "RPL37P23" "GAPDHP38" "RP11-382J24.2" "PSMC1P9"
## [25] "MIR3661" "AC024592.12"
## [1] 15
## [1] "NOP16" "NTHL1" "WDR7" "THOC5" "FAHD2A"
## [6] "NENF" "METTL8" "EMG1" "IMP4" "C19orf47"
## [11] "WDR43" "ZFP62" "ZNF770" "ZBTB48" "UAP1"
## [16] "SGSM2" "RPL32" "EPB41" "CXCR5" "ZNF589"
## [21] "RPS26" "SELM" "RP11-51J9.5"
## [1] 16
## [1] "REC8" "DHRS12" "GDAP1" "PRR4"
## [5] "SCPEP1" "ORMDL2" "RRM2" "MZT2A"
## [9] "ASB8" "HIST1H4C" "SLC26A6" "RP11-386G11.10"
## [13] "RGCC" "CPQ" "FOXP1" "PMEPA1"
## [17] "FAM117B" "NPAT" "TC2N" "GPR183"
## [21] "PLK3" "GOLGA8A" "SATB1" "TSC22D2"
## [1] 17
## [1] "NDUFAF7" "NSMAF" "IL4R" "USP48" "UTP6" "PTP4A1" "MYB"
## [8] "PGPEP1" "PPCDC" "NARF" "PMAIP1" "PPOX" "SEC24D" "FCGR3B"
## [15] "FBXO22" "ZNF232" "GNG4" "BOLA1" "CAPN12" "FCGR3A" "LEF1"
## [22] "GNAQ" "DHRS3" "NR1D2"
## [1] 18
## [1] "DUSP12" "AAAS" "DHPS" "NUP107" "GALE" "NUP85"
## [7] "COQ3" "FHOD1" "ASNSD1" "UCK2" "LPP" "CETN3"
## [13] "VPS37A" "GALK2" "AGPAT6" "NFU1" "TMEM126A" "CTDNEP1"
## [19] "UCKL1" "ATP5J2" "ABHD14A" "GGT7" "OBSCN"
## [1] 19
## [1] "RP3-324O17.4" "MDGA1" "PDE6B" "SLC35A5"
## [5] "GSTM4" "LRTOMT" "MYL5" "XXbac-B562F10.11"
## [9] "GS1-124K5.2" "GYG1P3" "AC115617.2" "GOT2P3"
## [13] "CTD-2301A4.3" "ACRC" "POU6F1" "TCEAL3"
## [17] "RP11-91K8.4" "ACTBP12" "RP1-187B23.1" "AP001468.1"
## [21] "ATP1B3-AS1" "RP11-44N11.1" "TMEM9B-AS1" "LINC00944"
## [25] "RP11-320M16.1" "CTD-2017D11.1"
## [1] 20
## [1] "TMEM134" "ZBTB8OS" "C2orf76" "RPSAP47"
## [5] "ZNF28" "TRGV10" "RPSAP54" "RP4-694B14.5"
## [9] "KANSL1-AS1" "RNU2-63P" "NPM1P19" "RP11-350G8.3"
## [13] "SAPCD1" "RP11-567G24.1" "AC093391.2" "EEF1A1P14"
## [17] "CDC42P1" "FAM200B" "AC018462.3" "EEF1A1P10"
## [21] "CTB-33G10.1" "TPM3P6" "RP11-1012A1.7" "RP13-638C3.4"
## [25] "RP11-209D14.4" "ACTBP9"
## [1] 21
## [1] "ICA1" "GBA2" "REXO1" "RABGGTA" "ILVBL"
## [6] "SRM" "PARP2" "FGFBP2" "MMS22L" "SPON2"
## [11] "COG5" "XRCC6BP1" "NT5DC1" "HIST1H2BC" "ZNF765"
## [16] "HIST2H2AA4" "HIST2H2BF" "TRAV14DV4" "LINC00493" "CNOT7P1"
## [21] "HIST1H2BN" "AC004069.2" "HIST1H3G" "HNRNPA1P50" "FRMD4A"
## [1] 22
## [1] "C1orf112" "AGA" "RNF13" "P2RX5" "GSR" "TYK2"
## [7] "GOSR2" "FIGNL1" "IDH1" "TAMM41" "TOMM40L" "B2M"
## [13] "AFMID" "KNTC1" "ENTPD5" "TMSB4X" "TREX1" "RGPD5"
## [19] "DKK3" "PPP2R5C" "STK17B" "EPHA1" "NELL2" "MALAT1"
## [1] 23
## [1] "ZNF268" "RRNAD1" "THAP2" "SNHG11"
## [5] "EIF2S3L" "CATSPER2P1" "TRAV35" "RP11-383G10.3"
## [9] "CALM2P3" "RPS12P26" "AC090804.1" "SKP1P1"
## [13] "RPS11P5" "CTC-338M12.4" "MAPKAPK5-AS1" "RP11-446E9.1"
## [17] "RP11-32B5.1" "AP000476.1" "FAM21FP" "RP11-394D2.1"
## [21] "RBBP4P1" "RP11-638I2.10" "CTD-2022H16.3" "RP11-304L19.5"
## [25] "RP11-265N6.3" "AC006129.4"
## [1] 24
## [1] "MED24" "ZNRD1" "POLR2I" "NSMCE4A"
## [5] "EPAS1" "UXT" "SLC41A2" "CLSTN3"
## [9] "TBCD" "MFSD6" "PPP4R1" "ALG8"
## [13] "MED11" "POLR2H" "IL15" "MEI1"
## [17] "LCORL" "TMEM107" "PPARA" "TRGV3"
## [21] "MRPL33" "RP11-33B1.1" "RP11-416A17.6" "MIR3615"
## [25] "RP11-297D21.4"
## [1] 25
## [1] "MTHFS" "DRAM2" "RHEBL1" "LRRC45"
## [5] "NME6" "PIGW" "MT1X" "ZNF720"
## [9] "TRBV4-2" "TRAV19" "ANAPC10P1" "RSC1A1"
## [13] "RP11-122G18.7" "RP11-350G13.1" "RP11-119F19.2" "NPM1P34"
## [17] "AC104820.2" "RP11-262H14.3" "NDUFA9P1" "RPSAP4"
## [21] "WDR65" "RP11-179A18.1" "TRGV7" "CTB-4E7.1"
## [25] "AL161784.1" "RP11-705C15.5"
## [1] 26
## [1] "TNFRSF9" "EVC" "NFE2L1" "CRTAM"
## [5] "C3orf14" "SMIM19" "RP11-254B13.4" "BACH2"
## [9] "NBPF14" "NR4A2" "AMICA1" "NBPF10"
## [13] "AC018720.10" "NAA16" "CHD2" "TSHZ2"
## [17] "TTC3" "PLGLB1" "KLHL25" "NBPF16"
## [21] "AC084018.1" "HCG4P5" "MTND4P12" "RP11-335G20.7"
## [25] "SLC7A5P1"
## [1] 27
## [1] "MBNL3" "FAH" "SNX8" "SCRN2"
## [5] "FUOM" "OXSM" "FAM122B" "DBF4B"
## [9] "DNASE1" "RP3-395M20.8" "DBNDD2" "AP000620.1"
## [13] "TPMTP1" "PLXND1" "AOAH" "CDC42EP3"
## [17] "ZMAT1" "RPS3AP26" "RP11-572P18.1" "RPL10P3"
## [21] "RPL9P8" "RPL3P4" "RPS3AP6" "RPL9P9"
## [25] "RPL9P7"
## [1] 28
## [1] "EGR2" "IL10" "TNFAIP8L2" "C19orf55"
## [5] "CMAHP" "ARHGAP11B" "ZNF257" "AC018804.7"
## [9] "AC009403.2" "LYPLA1P3" "AC012318.3" "RP4-742C19.12"
## [13] "ZNF826P" "AC011747.4" "ZEB1-AS1" "RP11-271C24.3"
## [17] "SRP14-AS1" "GMPSP1" "RP11-889L3.4" "MIR146A"
## [21] "SF3A3P2" "USP30-AS1" "TRAV30" "EFTUD1P1"
## [25] "RP11-265N6.2" "RIMKLB"
## [1] 29
## [1] "RNF10" "SMG6" "MICALL1" "GMPR2" "CNOT2" "MTFR1L"
## [7] "APTX" "CASP1" "HAUS2" "KSR1" "MAP3K6" "LIMD1"
## [13] "C2orf44" "DALRD3" "PCGF5" "CNOT10" "EIF4ENIF1" "ZNF544"
## [19] "TNRC6C" "TNRC6B" "CNOT6L" "BTG2" "PLA2G4B"
## [1] 30
## [1] "CHI3L2" "OCEL1" "NHP2P1" "IL18RAP"
## [5] "C2orf43" "FAM45A" "MTERF" "DTD2"
## [9] "NUDT7" "C9orf89" "ADCK5" "EFCAB4A"
## [13] "SLC9A9" "ZNF525" "TRGV5" "TRBV9"
## [17] "TRDV1" "TRDC" "RP4-800M22.1" "RPL19P21"
## [21] "ADH5P4" "AC144530.1" "STARD4-AS1" "RP11-317N8.4"
## [25] "RP11-1094M14.7" "RP11-282O18.6"
## [1] 31
## [1] "Z97634.3" "RASGRP2" "TCF7" "MAN1C1"
## [5] "ACVR2A" "CCR7" "C1orf162" "PLAC8"
## [9] "LDLRAP1" "PLXDC1" "TMEM150A" "CD248"
## [13] "YPEL2" "TRABD2A" "MIR4461" "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB" "CHRM3-AS2" "WHAMMP2"
## [21] "RP11-747H7.3" "RP11-1000B6.3" "KCNQ1OT1" "RP1-313I6.12"
## [25] "RP11-434H6.7"
## [1] 32
## [1] "CCL3" "RABGAP1" "GNPTAB" "SLC12A4" "CCL4" "GCHFR"
## [7] "PRSS23" "TMPRSS3" "SLC39A13" "DNAJC18" "ETFDH" "METTL18"
## [13] "ZNF80" "PDDC1" "WRB" "TNFRSF18" "CCL4L2" "AGER"
## [19] "MSH5" "UBE2D3P2" "MIR142" "PHLDB3" "PER1" "CD55"
## [1] 33
## [1] "CD200" "C14orf93" "TFDP2" "YIPF2"
## [5] "NDUFAF6" "PAQR4" "TMEM155" "LAIR2"
## [9] "TRANK1" "ZNF678" "EDARADD" "CRYGS"
## [13] "LINC00484" "BHLHE40-AS1" "RP11-305L7.3" "RP4-728D4.2"
## [17] "TRAV1-2" "RP11-493L12.6" "PMF1-BGLAP" "DGKA"
## [21] "MAK" "RP11-514P8.6" "RPS26P6" "HLA-W"
## [25] "RP13-488H8.1"
## [1] 34
## [1] "POLD3" "PTPN4" "UBXN8" "IFNG" "RCOR3" "NR2C1" "SNX14"
## [8] "GPN2" "FAM50B" "MITD1" "PPP1R32" "C7orf55" "ATPAF2" "CADM1"
## [15] "SCML1" "TXK" "CLDND1" "ABLIM1" "SLC38A1" "NEK1" "FBXO32"
## [22] "POLR2J3" "LDOC1" "HLA-J"
## [1] 35
## [1] "IFI27" "WDR53" "ZNF749" "FAM49A"
## [5] "ZNF649" "CPT1B" "TRAV8-2" "TRAV13-1"
## [9] "TRAV16" "TRAV29DV5" "PDCL3P5" "NPM1P32"
## [13] "RP1-102E24.1" "RPS19P1" "PSMA6P1" "PTGES3P2"
## [17] "RP3-340B19.5" "PRDX3P1" "RP11-288E14.2" "RPL7AP31"
## [21] "RP11-81H14.2" "MTRNR2L3" "RP11-511H9.4" "RPPH1"
## [25] "AC006483.1" "LUZP6"
## [1] 36
## [1] "CDKL1" "TTLL4" "MGAT4A" "HECA" "RCAN3"
## [6] "NR4A3" "PCNXL2" "RASGEF1B" "TIPARP" "PRMT10"
## [11] "FILIP1L" "ZBTB20" "RGPD6" "DENND5A" "ANKRD37"
## [16] "SELL" "FAM169A" "AC021593.1" "MTND1P23" "LINC00674"
## [21] "PSMD6-AS2" "RP11-285F7.2" "ZNF10" "QRSL1P3"
## [1] 37
## [1] "GCFC2" "OAS1" "GZMB" "ENO3"
## [5] "NCOA7" "GBP1" "MT2A" "RSAD2"
## [9] "SPPL2A" "IRF8" "SFR1" "SLAMF8"
## [13] "AMDHD2" "GNGT2" "KIR3DL1" "ITGAM"
## [17] "NINJ2" "SWI5" "PRF1" "RP11-365H23.1"
## [21] "KIR2DS4" "PTGES3P1" "AKAP2" "KIR2DL3"
## [25] "SERHL2"
## [1] 38
## [1] "PAFAH1B1" "LIN7B" "PON2" "KLRB1" "CCDC77"
## [6] "ACTR10" "FOPNL" "KLRC1" "AHI1" "BORA"
## [11] "CXCL13" "PANK4" "MGAT4B" "SLC38A9" "CEP57L1"
## [16] "HLA-DQA1" "CCL4L1" "KLRC2" "METTL6" "TCTEX1D2"
## [21] "KIR3DL2" "RP11-345J4.6" "MPP7"
## [1] 39
## [1] "TNFSF10" "PTGER2" "IFI44L" "IFI44" "XCL1"
## [6] "XCL2" "TRPT1" "CX3CR1" "MT1E" "HOPX"
## [11] "RP11-23P13.6" "ZNF683" "NAP1L4P1" "MTHFD2P7" "EEF1GP1"
## [16] "C10orf128" "TRBV20-1" "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"
## [21] "TSEN15P1" "SNRPEP4" "MIR155HG" "RNU1-125P" "AL358333.1"
## [1] 40
## [1] "EVI5" "WIPI1" "LTBP4" "RGS1"
## [5] "PMM1" "FADS2" "IRF4" "BCAS3"
## [9] "PELP1" "AMFR" "CXCR6" "TRAV12-2"
## [13] "TMEM66" "ATXN7" "NPIPB3" "EIF1"
## [17] "NPIPB4" "GPRASP1" "KLRK1" "MTND2P28"
## [21] "CTD-2328D6.1" "RPL41" "NPIPB5" "MTATP6P1"
## [25] "CTD-2031P19.4"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "MTIF2" "KHSRP" "MRPS33" "NDUFAF5" "CDK5RAP1" "EARS2"
## [7] "MTFMT" "SARS2" "GTPBP10" "DHX58" "ATPAF1" "NDUFAF4"
## [13] "C6orf203" "MTO1" "MRRF" "MALSU1" "MRPL55" "NDUFS4"
## [19] "PHAX" "MRPL48" "ZNF431" "MRPL23" "CCDC109B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 2.012426e-10 1.0000000
## 986 translation 1.162489e-06 0.9999999
## numDEInCat numInCat FDR
## 495 7 9 2.056700e-07
## 986 9 46 5.940318e-04
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 0.000000e+00
## 1307 mitochondrial rna metabolic process 2.723763e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1 11 16 0.0000000000
## 1311 1 9 13 0.0000000000
## 1307 1 5 7 0.0003710674
##
## [1] "set_2"
## [1] "CENPQ" "CENPO" "ZNF816" "RPS17" "TNF" "APBA2" "RPL34"
## [8] "RPS12" "RASGRF2" "EGR1" "RPL21" "FOSB" "JUND" "SORL1"
## [15] "RPS27A" "RPL9" "RBKS" "JUNB" "RPLP2" "RPS27" "DNHD1"
## [22] "RPS23" "RPS18"
## $reactome
## category
## 890 srp dependent cotranslational protein targeting to membrane
## 256 eukaryotic translation initiation
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 255 eukaryotic translation elongation
## 691 regulation of expression of slits and robos
## 547 nonsense mediated decay nmd
## 808 selenoamino acid metabolism
## 117 cellular response to starvation
## 869 signaling by robo receptors
## 387 influenza infection
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 890 1.367410e-08 1 10 29
## 256 1.878780e-08 1 10 30
## 734 1.912613e-08 1 10 30
## 255 2.552031e-08 1 10 31
## 691 2.648305e-08 1 10 31
## 547 2.815049e-08 1 10 31
## 808 3.633881e-08 1 10 32
## 117 4.808493e-08 1 10 33
## 869 4.815877e-08 1 10 33
## 387 1.736204e-07 1 10 37
## FDR
## 890 4.794966e-06
## 256 4.794966e-06
## 734 4.794966e-06
## 255 4.794966e-06
## 691 4.794966e-06
## 547 4.794966e-06
## 808 5.305467e-06
## 117 5.468696e-06
## 869 5.468696e-06
## 387 1.774400e-05
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 515 cytoplasmic translation 3.832737e-09 1.0000000
## 3637 response to salt 2.992022e-06 0.9999999
## 403 cellular response to salt 1.000833e-05 0.9999999
## numDEInCat numInCat FDR
## 515 10 33 0.0000156644
## 3637 5 11 0.0061141980
## 403 4 7 0.0136346749
##
## $immune
## category
## 2358 gse26156 double positive vs cd4 single positive thymocyte up
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 1940 gse22886 naive bcell vs dc up
## 4064 gse42088 uninf vs leishmania inf dc 2h dn
## 1725 gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2358 6.228214e-07 1.0000000 8 36
## 1944 9.271724e-07 1.0000000 7 25
## 1974 7.059308e-06 0.9999996 7 33
## 1940 2.645149e-05 0.9999985 6 28
## 4064 3.236369e-05 0.9999980 6 29
## 1725 3.569177e-05 0.9999985 5 17
## 54 6.796412e-05 0.9999952 6 32
## FDR
## 2358 0.002363826
## 1944 0.002363826
## 1974 0.011998471
## 1940 0.030332052
## 4064 0.030332052
## 1725 0.030332052
## 54 0.049507010
##
## [1] "set_3"
## [1] "MAD1L1" "SLC25A14" "ERCC2" "IMPDH1" "C17orf75" "GTF2H3"
## [7] "CDC20" "DCAF4" "CKS2" "MCEE" "UROD" "PDZD2"
## [13] "CCNB1" "CDK7" "COPS3" "CCNB2" "MTHFD2L" "POLE"
## [19] "BTLA" "HIST1H4J" "PRIM1" "C1orf85" "STK19" "MUC20"
## $reactome
## category
## 326 global genome nucleotide excision repair gg ner
## 967 transcription coupled nucleotide excision repair tc ner
## 574 nucleotide excision repair
## 284 formation of tc ner pre incision complex
## 158 cyclin a b1 b2 associated events during g2 m transition
## 766 rna polymerase i transcription initiation
## 767 rna polymerase i transcription termination
## 283 formation of rna pol ii elongation complex
## 286 formation of the early elongation complex
## 370 hiv transcription elongation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 326 3.628575e-05 0.9999986 5 14
## 967 3.695727e-05 0.9999986 5 14
## 574 1.082683e-04 0.9999945 5 17
## 284 1.614574e-04 0.9999948 4 10
## 158 2.907588e-04 0.9999959 3 5
## 766 2.937602e-04 0.9999958 3 5
## 767 2.937602e-04 0.9999958 3 5
## 283 2.964478e-04 0.9999958 3 5
## 286 2.964478e-04 0.9999958 3 5
## 370 2.964478e-04 0.9999958 3 5
## FDR
## 326 0.01888517
## 967 0.01888517
## 574 0.02754269
## 284 0.02754269
## 158 0.02754269
## 766 0.02754269
## 767 0.02754269
## 283 0.02754269
## 286 0.02754269
## 370 0.02754269
##
## $go_bp
## category over_represented_pvalue
## 1318 mitotic cell cycle phase transition 5.518124e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1318 0.9999996 8 42 0.02255257
##
## [1] "set_18"
## [1] "DUSP12" "AAAS" "DHPS" "NUP107" "GALE" "NUP85"
## [7] "COQ3" "FHOD1" "ASNSD1" "UCK2" "LPP" "CETN3"
## [13] "VPS37A" "GALK2" "AGPAT6" "NFU1" "TMEM126A" "CTDNEP1"
## [19] "UCKL1" "ATP5J2" "ABHD14A" "GGT7" "OBSCN"
## $reactome
## category
## 562 nuclear envelope breakdown
## 400 interactions of rev with host cellular proteins
## 401 interactions of vpr with host cellular proteins
## 567 nuclear import of rev protein
## 694 regulation of glucokinase by glucokinase regulatory protein
## 904 sumoylation of sumoylation proteins
## 906 sumoylation of ubiquitinylation proteins
## 257 export of viral ribonucleoproteins from nucleus
## 901 sumoylation of dna replication proteins
## 903 sumoylation of rna binding proteins
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 562 2.461663e-05 0.9999996 4 9
## 400 4.158902e-05 0.9999998 3 4
## 401 4.158902e-05 0.9999998 3 4
## 567 4.158902e-05 0.9999998 3 4
## 694 4.158902e-05 0.9999998 3 4
## 904 4.158902e-05 0.9999998 3 4
## 906 4.158902e-05 0.9999998 3 4
## 257 9.827123e-05 0.9999991 3 5
## 901 1.066252e-04 0.9999990 3 5
## 903 1.067353e-04 0.9999990 3 5
## FDR
## 562 0.006071997
## 400 0.006071997
## 401 0.006071997
## 567 0.006071997
## 694 0.006071997
## 904 0.006071997
## 906 0.006071997
## 257 0.010005313
## 901 0.010005313
## 903 0.010005313
##
## [1] "set_21"
## [1] "ICA1" "GBA2" "REXO1" "RABGGTA" "ILVBL"
## [6] "SRM" "PARP2" "FGFBP2" "MMS22L" "SPON2"
## [11] "COG5" "XRCC6BP1" "NT5DC1" "HIST1H2BC" "ZNF765"
## [16] "HIST2H2AA4" "HIST2H2BF" "TRAV14DV4" "LINC00493" "CNOT7P1"
## [21] "HIST1H2BN" "AC004069.2" "HIST1H3G" "HNRNPA1P50" "FRMD4A"
## $reactome
## category
## 356 hdacs deacetylate histones
## 355 hcmv late events
## 352 hats acetylate histones
## 353 hcmv early events
## 354 hcmv infection
## 10 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 63 assembly of the orc complex at the origin of replication
## 122 chromatin modifications during the maternal to zygotic transition mzt
## 209 dna methylation
## 249 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 356 1.991681e-05 0.9999995 5 11
## 355 5.548716e-05 0.9999980 5 15
## 352 7.931066e-05 0.9999968 5 16
## 353 9.596559e-05 0.9999959 5 17
## 354 1.234231e-04 0.9999944 5 18
## 10 2.169060e-04 0.9999935 4 9
## 63 2.169060e-04 0.9999935 4 9
## 122 2.169060e-04 0.9999935 4 9
## 209 2.169060e-04 0.9999935 4 9
## 249 2.169060e-04 0.9999935 4 9
## FDR
## 356 0.01847316
## 355 0.01847316
## 352 0.01847316
## 353 0.01847316
## 354 0.01847316
## 10 0.01847316
## 63 0.01847316
## 122 0.01847316
## 209 0.01847316
## 249 0.01847316
##
## [1] "set_29"
## [1] "RNF10" "SMG6" "MICALL1" "GMPR2" "CNOT2" "MTFR1L"
## [7] "APTX" "CASP1" "HAUS2" "KSR1" "MAP3K6" "LIMD1"
## [13] "C2orf44" "DALRD3" "PCGF5" "CNOT10" "EIF4ENIF1" "ZNF544"
## [19] "TNRC6C" "TNRC6B" "CNOT6L" "BTG2" "PLA2G4B"
## $reactome
## category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 981 transcriptional regulation by tp53
## 954 tp53 regulates transcription of cell cycle genes
## 172 deadenylation of mrna
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952 3.560203e-06 1.0000000 4 6
## 981 7.267698e-06 0.9999996 7 35
## 954 1.346275e-05 0.9999998 4 8
## 172 6.478048e-05 0.9999996 3 4
## FDR
## 952 0.003638527
## 981 0.003713794
## 954 0.004586311
## 172 0.016551413
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 1912 nuclear transcribed mrna catabolic process
## 3702 rna destabilization
## 2380 positive regulation of mrna metabolic process
## 3201 regulation of mrna catabolic process
## 1372 mrna catabolic process
## 1456 negative regulation of amide metabolic process
## 3202 regulation of mrna metabolic process
## 3700 rna catabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 3.599968e-11 1.0000000 7 8
## 1913 6.556969e-10 1.0000000 7 10
## 1912 9.780452e-10 1.0000000 8 15
## 3702 1.149893e-08 1.0000000 7 14
## 2380 4.080189e-08 1.0000000 7 16
## 3201 8.518372e-08 1.0000000 7 17
## 1372 9.073724e-08 1.0000000 8 24
## 1456 1.605856e-07 1.0000000 8 29
## 3202 4.392593e-07 1.0000000 7 21
## 3700 1.161380e-06 0.9999999 8 29
## FDR
## 1917 1.471307e-07
## 1913 1.332424e-06
## 1912 1.332424e-06
## 3702 1.174903e-05
## 2380 3.335146e-05
## 3201 5.297759e-05
## 1372 5.297759e-05
## 1456 8.203918e-05
## 3202 1.994725e-04
## 3700 4.746562e-04
##
## [1] "set_31"
## [1] "Z97634.3" "RASGRP2" "TCF7" "MAN1C1"
## [5] "ACVR2A" "CCR7" "C1orf162" "PLAC8"
## [9] "LDLRAP1" "PLXDC1" "TMEM150A" "CD248"
## [13] "YPEL2" "TRABD2A" "MIR4461" "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB" "CHRM3-AS2" "WHAMMP2"
## [21] "RP11-747H7.3" "RP11-1000B6.3" "KCNQ1OT1" "RP1-313I6.12"
## [25] "RP11-434H6.7"
## $immune
## category
## 3016 gse32986 unstim vs gmcsf stim dc up
## 2390 gse26495 naive vs pd1high cd8 tcell up
## 3005 gse32986 gmcsf vs gmcsf and curdlan lowdose stim dc dn
## 1702 gse21670 il6 vs tgfb and il6 treated cd4 tcell up
## 4341 gse4984 lps vs vehicle ctrl treated dc up
## 3596 gse3982 basophil vs cent memory cd4 tcell dn
## 2392 gse26495 naive vs pd1low cd8 tcell up
## 1799 gse22045 treg vs tconv dn
## 4400 gse5542 untreated vs ifna treated epithelial cells 24h dn
## 3391 gse37301 common lymphoid progenitor vs rag2 ko nk cell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3016 1.063057e-06 1.0000000 6 25
## 2390 3.744405e-06 0.9999999 6 30
## 3005 4.063936e-06 0.9999998 6 32
## 1702 5.818615e-06 0.9999998 5 22
## 4341 7.492212e-06 0.9999998 5 19
## 3596 1.233604e-05 0.9999998 4 10
## 2392 2.378461e-05 0.9999991 5 24
## 1799 7.385562e-05 0.9999978 4 15
## 4400 7.792784e-05 0.9999976 4 17
## 3391 8.332639e-05 0.9999975 4 15
## FDR
## 3016 0.005420529
## 2390 0.006907337
## 3005 0.006907337
## 1702 0.007417279
## 4341 0.007640557
## 3596 0.010483582
## 2392 0.017325391
## 1799 0.042488128
## 4400 0.042488128
## 3391 0.042488128
##
## [1] "set_37"
## [1] "GCFC2" "OAS1" "GZMB" "ENO3"
## [5] "NCOA7" "GBP1" "MT2A" "RSAD2"
## [9] "SPPL2A" "IRF8" "SFR1" "SLAMF8"
## [13] "AMDHD2" "GNGT2" "KIR3DL1" "ITGAM"
## [17] "NINJ2" "SWI5" "PRF1" "RP11-365H23.1"
## [21] "KIR2DS4" "PTGES3P1" "AKAP2" "KIR2DL3"
## [25] "SERHL2"
## $immune
## category over_represented_pvalue
## 55 gaucher pbmc yf vax stamaril unknown age 7dy up 2.244661e-07
## 45 gaucher pbmc yf vax stamaril unknown age 10dy up 1.517796e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 55 1.000000 9 45 0.001144553
## 45 0.999999 7 39 0.038696207
##
## [1] "set_39"
## [1] "TNFSF10" "PTGER2" "IFI44L" "IFI44" "XCL1"
## [6] "XCL2" "TRPT1" "CX3CR1" "MT1E" "HOPX"
## [11] "RP11-23P13.6" "ZNF683" "NAP1L4P1" "MTHFD2P7" "EEF1GP1"
## [16] "C10orf128" "TRBV20-1" "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"
## [21] "TSEN15P1" "SNRPEP4" "MIR155HG" "RNU1-125P" "AL358333.1"
## $reactome
## category over_represented_pvalue
## 127 class a 1 rhodopsin like receptors 1.176486e-05
## 349 gpcr ligand binding 2.673622e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 127 0.9999999 4 19 0.01202368
## 349 0.9999996 4 23 0.01366221Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958520 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19169159 146.3 59533611 454.3 65536 78485130 598.8## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1